[gmx-users] Representative structure of a long simulation

[Marc Baaden]

Hi,

the following might be a trivial/basic question, but I would like
to get as many comments/different ideas/views as possible.

I have a long (10 ns) simulation of a membrane protein system, and
would like to use one protein structure out of this simulation as
starting point for some further (simple) studies. So I am somehow
looking for the most "representative" structure out of these 10 ns.

My idea was to use the clustering approach, and go for the cluster
which is predominant (in the sense of nb of occurrences), using its
central structure.

Nevertheless there is simply too much data (10 ns * high save frequency)
too run a cluster analysis on the whole thing. So what is the right way
in order not to "miss" anything ?

Or would you suggest another approach ? (eg based on energies ? ..)

thanks for your comments,
Marc Baaden
-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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